Activity-based protein profiling (ABPP) is an emerging, powerful strategy to identify enzymes in the proteome. Currently, the success of ABPP is dependent upon carefully designed probes that consist of 3 components: (a) a reactive group that enables the covalent attachment of the probe to an enzyme, (b) a tag that facilitates the detection and/or purification of the enzyme-probe conjugate, and (c) a linker that chemically attaches the reactive group to the tag. The reactive groups are chosen based on their ability to react with a related family of enzymes. A considerable amount of background enzymological information is necessary to design the ABPP probes. In addition, this method cannot easily be used to profile non-catalytic proteins. Many biologically significant proteins, including regulatory proteins, transport proteins, structural proteins, and receptors, exhibit no catalytic activity. CoA-dependent enzymes and proteins are a large family, encompassing ~4% of all known proteins. Many members of this family are aberrantly expressed in a diversity of cancers, examples being the over-expression of stearoyl-CoA desaturase in breast cancer and the under-expression of acyl-CoA oxidase in liver cancer. The correlations between the anomalous expression of CoA-dependent proteins and cancer were generally determined by assaying for the expression levels of individual family members in a specific cancer. Given the size and importance of the CoA-dependent protein family, a better strategy to understand how the defective expression of these proteins is involved in cancer initiation and proliferation would be to profile the CoA-dependent proteins in cancer proteomes. Proteome profiles of CoA-dependent proteins will lead to innovative strategies for the early diagnosis of cancer and will identify new targets for the design of novel anticancer drugs. Our solution to the problem of profiling CoA-dependent proteins is to synthesize a set of ABPP probes of 2 broad classes, biotinylated acyl-CoA analogs with and without an attached azido group. The profiling probes we will produce are based solely on the CoA and acyl-CoA ligands that bind to CoA-dependent proteins, a technique we call binding-based proteome profiling (BBPP). The success of BBPP will substantially broaden the application of protein profiling methods to enzymes for which we know little beyond the substrates and products of the reaction and to proteins that do not have a catalytic function - a significant advance in the field of proteome profiling. [unreadable] [unreadable]